The present invention relates to the diagnosis of cancer, and more specifically to the use of characteristic patterns of gene expression by circulating cells of the immune system and/or circulating cancer cells and/or tumor cells as a method of diagnosis.
Microarrays of several different types have been used to characterize cancer types in patients, most often to distinguish the tissue of origin or a tumor (Ramaswami et al, 2001, Proc. Natl. Acad. Sci. USA, 98:15149-54) or original cell type of a leukemia (Golub et al, 1999 Science, 218:531-7). In contrast, current practice of cancer diagnosis usually depends on imaging methods, e.g., chest X-rays, histological studies, mammograms, and the like. More recently efforts have been made to detect proteins characteristic of certain cancers in serum, e.g., PSA for prostate cancer.
cDNA arrays have been used to characterize the components of the immune system, as purified cells (Hamalainen, H., et al. 2001 Genome Biol 2: RES.0022), as cell lines, as mixtures of peripheral blood mononuclear cells (PBMC) (Alizadeh, A. A., and L. M. Staudt, 2000 Curr Opin Immunol 12:219-2255), and in whole blood (Whitney, A. R, et al., 2003 Proc Natl Acad Sci USA 100:1896-19016). However most attempts to describe the immune response to cancer, especially tumors, has made use of monoclonal antibodies to characterize the type and differentiation state of B-cells, T-cells, natural killer (NK) cells and dendritic cells, which infiltrate tumors. The reflection of this infiltration is observed by activated cells in the peripheral blood. See, e.g., Fracchia, A., et al, 1987 Respiration 51:161-169; Domagala-Kulawik, J., et al., 2001 Diagn. Cytopathol., 25:208-213; Mazzoccoli, G., et al. 1999. In Vivo 13:205-209; and Lee, P. P. et al., 1999 Nat Med 5:677-6850.
A number of microarray studies have identified genes that appear to be useful for diagnosis of a variety of different cancers. Changes in individual gene products have been reported on tumor infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells (PBMCs) from cancer patients. For example, the loss in colorectal adenocarcinoma patients of the Zeta (signal transducing) chain of the TCR/CD3 complex of T-cells in a tumor-stage specific manner from both TILs and PBLs was reported (Choi, S. H., et al., 1998 Cancer Immunol Immunother 45:299-305). The Zeta-associated kinase, p59 fyn, was also reduced in PBMC from patients relative to controls. Numerous receptors have been shown to function in targeting lymphocytes either to skin, on the one hand, or various mucosa on the other. These include the cutaneous lymphocyte antigen (CLA) and chemokine receptors CCR4 and CCR10/CTACK expressed on skin-homing lymphocytes, the integrin a4b7 which directs homing to the gastric mucosa, and integrin a4b1 expressed on lymphocytes which are directed to non-intestinal mucosa such as those of the lungs (see, e.g., Kunkel, E. J., and E. C. Butcher. 2000 Immunity 16:1-4). In addition to these T-cell gene products, B-cells have been reported to express different heavy chains depending on their target tissue. NK T-cells, which are associated with the IL-12 dependent rejection of some tumors (Cui, J., et al. 1997 Science 278:1623-16263) express different sets of Va and Vb T-cell receptor chains that are associated with homing to different lymphoid organs (e.g. bone marrow, liver, spleen (Eberle, J., et al. 1999 J Invest Dermatol 112:925-9324).
Few of these above-noted microarray studies translate the results to assays suitable for clinical use. For example, a “gene expression ratio” method differentiates patients with mesotheliomas from adenocarcinomas of the lung by using simple ratios of pairs of expressed genes determined by PCR (Gordon, G. J., et al, 2002 Cancer Res, 62: 4963-4967). This method is dependent on being able to identify gene pairs whose differences in expression levels are very highly significant between the 2 tumor types being compared. These types of differences might be expected where the organ or cell-type of tumor origin are different.
Cutaneous T-cell Lymphoma (CTCL), the most common of the T-cell lymphomas, is a non-Hodgkin lymphoma of epidermotropic lymphocytes. Approximately 1500-2000 new cases are reported in the United States each year. Causative roles in the development of CTCL have been suggested for various environmental factors and infectious agents, but the etiology of the disease remains unknown (Li, G et al, J. Invest. Dermatol., 107:308-313; Kim, Y. H., and R. T. Hoppe. 1999 Semin Oncol, 26:276-289). CTCL is characterized by the accumulation of malignant cells with a low mitotic index, suggesting that the regulatory defect allowing these cells to accumulate may reside in the apoptotic pathways (Dereure, O., et al, 2000 Brit. J. Dermatol. 143:1205-1210; Edelson, R. L. 2001 Ann N Y Acad Sci 941:1-11). Mycosis fungoides (MF) and Sezary syndrome (SzS) are the two major clinical variants of CTCL (Kim, Y. H. and Hoppe, R. T. 1999 Semin Oncol, 26: 276-289 (Kim III); Kim, Y. H. et al, 1996 Arch. Dermatol., 132: 1309-1313 (Kim II); and Diamandidou, E. et al. 1996 Blood, 88: 2385-2409).
MF is skin associated and progresses through increasing cutaneous, and finally organ involvement. Although treatable in early stages, MF is frequently misdiagnosed because of similarities to more benign forms of skin disease. Even with early diagnosis, 10% of MF patients who present with limited disease and about 25% of those with extensive patches or plaques will develop progressive disease, eventually succumbing despite extensive therapy (Kim I; Kim, et al 1999 Arch Dermatol 135:26-32 (Kim IV). SzS, a leukemic and erythrodermic variant of CTCL, is characterized by the presence of circulating lymphocytes with atypical cerebriform nuclei (Sezary cells) in the skin, lymph nodes, and peripheral blood. It is a more aggressive form of CTCL, which is associated with a poor prognosis and with a mean survival of three years from the time of diagnosis. Immunophenotyping and genotyping of Sezary cells indicates that they arise as a clonal expansion of mature helper memory T-cells (Dereure, cited above and Edelson, cited above). They express cytokines characteristic of T-helper type 2 (Th2) cells, including IL-4, IL-5, and IL-10 (Dummer, R., et al, 1996 Blood 88:1383-1389; Nickoloff, B. J., et al, 1994 Clin Immunol Immunopathol 73:63-68; Rook, A. H., et al 1993 Arch Dermatol 129:486-489) and fail to express Th-1 cytokines, IL12, and IFN-γ (Vowels, B. R., et al., 1994 J Invest Dermatol 103:669-673). Patients with MF can have blood findings typically observed in SzS, and in rare cases MF can evolve into SzS, confirming a close relationship between the two conditions.
In both MF and SzS, early detection and treatment is directly correlated with outcome (Duvic, M. Clin Lymphoma, 1 Suppl 1: S15-20, 2000; Foss, F. M. 1 Suppl 1: S9-14, 2000; Kim, Y. H. et al, Arch Dermatol, 131: 10031008, 1995 (Kim 1). However, although CTCL is readily treatable in early stages, this relatively rare cancer can be difficult to diagnose because of similarities to a variety of benign skin diseases and frequently goes undetected for years. Therapies using biological response modifiers, such as extra-corporeal photopheresis and IFN-α, have improved survival of patients with SzS (Rook, A. H et al, 1999 J Investig Dermatol Symp Proc 4:85-90; Gottlieb, S. L et al., 1996 J Am Acad Dermatol 35:946-957). However, 50% of patients who present with advanced disease do not respond to therapy and 25% of those that respond initially will relapse and progress to fatal disease. There are presently no well-defined clinical markers for CTCL that permit an early identification of patients most likely to develop progressive disease.
There remains a need in the art for novel methods using gene expression as a useful diagnostic method for cancer, and in particular, for a more efficient and inexpensive method for detecting the presence of cancer in a normal population for purposes of screening, as a replacement for diagnostic imaging.